Protein profile

KP13_01039

putative adenine-specific methylase

Genome: KpKP13

Gene: AHE43433.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GVU0

Export view

Amino acids 334

Annotations 11

Features 22

PDB binders 1

Druggability 0.957

Overview

Basic information about this protein and its source genome.

Accession: KP13_01039
Assembly: Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene: AHE43433.1
Status: annotated
Amino acids: 334
Structure source: AlphaFold + ColabFold

2.1.1.298

GO:0009007 Catalysis of the reaction: S-adenosyl-L-methionine + DNA adenine = S-adenosyl-L-homocysteine + DNA 6-methylaminopurine. GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule. GO:0003676 Binding to a nucleic acid. GO:0032775 OBSOLETE. The covalent transfer of a methyl group to N-6 of adenine in a DNA molecule. GO:0006479 The addition of a methyl group to a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom. GO:0032259 The process in which a methyl group is covalently attached to a molecule.

Target profile

Computed evidence for target prioritization.

Human off-target: hit
Human identity (%): 29.004
Human E-value: 3.21e-14
Gut microbiome off-target: hit
Essential (DEG): Y
DEG identity (%): 60.596
DEG E-value: 1.86e-142
Localization: Cytoplasmic
ColabFold pLDDT: 92.33

Selected Druggability evidence

AlphaFold / UniProt model

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.957

Structure A0A0H3GVU0

Pocket Pocket 1

P2Rank 0.765

Structure A0A0H3GVU0

Pocket Pocket 1

ColabFold model

FPocket 0.911 · Pocket 1

P2Rank 0.778 · Pocket 1

Core conservation Conserved core gene

Roary core

CoreCruncher core

Gut microbiome 177 / 4744 genomes with a hit

Normalized 0.037

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 10 GO

Enzyme Commission (EC)

2.1.1.298

Gene Ontology (GO)

GO:0009007 Catalysis of the reaction: S-adenosyl-L-methionine + DNA adenine = S-adenosyl-L-homocysteine + DNA 6-methylaminopurine.
GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule.
GO:0003676 Binding to a nucleic acid.
GO:0032775 OBSOLETE. The covalent transfer of a methyl group to N-6 of adenine in a DNA molecule.
GO:0006479 The addition of a methyl group to a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom.
GO:0032259 The process in which a methyl group is covalently attached to a molecule.
GO:0008276 Catalysis of the transfer of a methyl group (CH3-) to a protein.
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
GO:0005840 An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.
GO:0036009 Catalysis of the reaction: L-glutaminyl-[protein] + S-adenosyl-L-methionine = N(5)-methyl-L-glutaminyl-[protein] + S-adenosyl-L-homocysteine + H+.

Sequence Features

Domain/signature hits from InterPro and related databases.

22 records

Show feature table

Start	End	DB	Term	Name
38	128	Gene3D	G3DSA:1.10.8.10	-
26	334	PANTHER	PTHR47806	50S RIBOSOMAL PROTEIN L3 GLUTAMINE METHYLTRANSFERASE
26	334	InterPro	IPR017127	Ribosomal protein L3-specific, glutamine-N5-methyltransferase
129	303	Gene3D	G3DSA:3.40.50.150	Vaccinia Virus protein VP39
129	303	InterPro	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily
129	303	FunFam	G3DSA:3.40.50.150:FF:000042	50S ribosomal protein L3 glutamine methyltransferase
37	319	NCBIfam	TIGR03533	50S ribosomal protein L3 N(5)-glutamine methyltransferase
37	319	InterPro	IPR017127	Ribosomal protein L3-specific, glutamine-N5-methyltransferase
39	317	SUPERFAMILY	SSF53335	S-adenosyl-L-methionine-dependent methyltransferases
39	317	InterPro	IPR029063	S-adenosyl-L-methionine-dependent methyltransferase superfamily
155	239	Pfam	PF05175	Methyltransferase small domain
155	239	InterPro	IPR007848	Methyltransferase small domain
22	331	PIRSF	PIRSF037167	Mtase_YfcB
22	331	InterPro	IPR017127	Ribosomal protein L3-specific, glutamine-N5-methyltransferase
30	324	Hamap	MF_02125	50S ribosomal protein L3 glutamine methyltransferase [prmB].
30	324	InterPro	IPR017127	Ribosomal protein L3-specific, glutamine-N5-methyltransferase
228	234	ProSitePatterns	PS00092	N-6 Adenine-specific DNA methylases signature.
228	234	InterPro	IPR002052	DNA methylase, N-6 adenine-specific, conserved site
39	326	NCBIfam	TIGR00536	HemK family protein methyltransferase
39	326	InterPro	IPR004556	Methyltransferase HemK-like
38	128	FunFam	G3DSA:1.10.8.10:FF:000022	50S ribosomal protein L3 glutamine methyltransferase
160	234	CDD	cd02440	AdoMet_MTases

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

Loading 3D structure...

Legend High Medium Low

Structural evidence

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry	Method	Resolution	Chain	Coverage	Links	Status
AlphaFold AF_A0A0H3GVU0	AlphaFold	—	—	full sequence	—	Viewing
ColabFold KP13_01039	ColabFold	—	—	full sequence	—	Loaded

Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET	Sticks	Spheres	Surfaces	Druggability	Labels	Zoom	Positions
1				0.957

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				10.2	0.548
2				6.22	0.311

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET	Sticks	Spheres	Surfaces	Druggability	Labels	Zoom	Positions
1				0.911
23				0.396

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK	Sticks	Spheres	Surfaces	Score	Probability	Labels	Zoom	Positions
1				10.14	0.545
2				6.83	0.35

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

51 records

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, use Open crystal to inspect it in the structure viewer.

No PDB structure with a co-crystallized ligand found for this exact protein.

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Ligand	Source crystal	UniProt (homolog)	MW · LogP · TPSA	Lipinski	PAINS	SMILES
MEQ	1NV8	Q9WYV8	160.2 Da LogP -1.08 TPSA 92.4	✓ Ro5	✓ Clean	`CNC(=O)CC[C@@H](C(=O)O)N`

Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL bioactivity data found for this exact protein.

Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).

No ChEMBL hits found through similar proteins.

Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).

Ligand	Tanimoto	MW · LogP · TPSA	Lipinski	PAINS	SMILES
ZINC1529737	0.714	218.2 Da LogP -1.23 TPSA 129.7	✓ Ro5	✓ Clean	`C[C@@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)O`
ZINC2384790	0.714	218.2 Da LogP -1.23 TPSA 129.7	✓ Ro5	✓ Clean	`C[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)O`
ZINC2560745	0.714	218.2 Da LogP -1.23 TPSA 129.7	✓ Ro5	✓ Clean	`C[C@@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)O`
ZINC2560989	0.714	218.2 Da LogP -1.23 TPSA 129.7	✓ Ro5	✓ Clean	`C[C@H](NC(=O)CC[C@@H](N)C(=O)O)C(=O)O`
ZINC2390999	0.655	275.3 Da LogP -1.99 TPSA 172.8	✓ Ro5	✓ Clean	`NC(=O)CC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)O`
ZINC2516115	0.613	246.3 Da LogP -0.60 TPSA 129.7	✓ Ro5	✓ Clean	`CC(C)[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)O`
ZINC13514803	0.606	347.3 Da LogP -1.88 TPSA 196.1	1 viol.	✓ Clean	`C[C@H](NC(=O)CC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=…`
ZINC1576202	0.600	204.2 Da LogP -1.62 TPSA 129.7	✓ Ro5	✓ Clean	`N[C@@H](CCC(=O)NCC(=O)O)C(=O)O`
ZINC3995565	0.600	204.2 Da LogP -1.62 TPSA 129.7	✓ Ro5	✓ Clean	`N[C@H](CCC(=O)NCC(=O)O)C(=O)O`
ZINC2504764	0.594	232.2 Da LogP -0.84 TPSA 129.7	✓ Ro5	✓ Clean	`CC[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)O`
ZINC3055005	0.591	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCC[C@H](N)C(=O)O)C(=O)O`
ZINC3055007	0.591	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC3055010	0.591	204.2 Da LogP -0.63 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC2391099	0.586	274.3 Da LogP -2.59 TPSA 178.6	✓ Ro5	✓ Clean	`NC(=O)CC[C@H](N)C(=O)N[C@@H](CCC(N)=O)C(=O)O`
ZINC1608689	0.576	202.3 Da LogP 0.09 TPSA 92.4	✓ Ro5	✓ Clean	`CCCCNC(=O)CC[C@H](N)C(=O)O`
ZINC2045835	0.576	202.3 Da LogP 0.09 TPSA 92.4	✓ Ro5	✓ Clean	`CCCCNC(=O)CC[C@@H](N)C(=O)O`
ZINC2384788	0.576	260.3 Da LogP -0.21 TPSA 129.7	✓ Ro5	✓ Clean	`CC(C)C[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)O`
ZINC12496578	0.571	275.3 Da LogP -2.12 TPSA 158.8	✓ Ro5	✓ Clean	`C[C@H](NC(=O)CC[C@H](N)C(=O)O)C(=O)NCC(=O)O`
ZINC2556600	0.567	217.2 Da LogP -1.83 TPSA 135.5	✓ Ro5	✓ Clean	`C[C@H](NC(=O)[C@@H](N)CCC(N)=O)C(=O)O`
ZINC1555366	0.565	232.3 Da LogP 0.15 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCCC[C@H](N)C(=O)O)C(=O)O`
ZINC1555367	0.565	232.3 Da LogP 0.15 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1555369	0.565	232.3 Da LogP 0.15 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1720127	0.565	218.3 Da LogP -0.24 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCC[C@H](N)C(=O)O)C(=O)O`
ZINC1720128	0.565	218.3 Da LogP -0.24 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC1720130	0.565	218.3 Da LogP -0.24 TPSA 126.6	✓ Ro5	✓ Clean	`N[C@H](CCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC13507519	0.563	234.2 Da LogP -2.26 TPSA 150.0	✓ Ro5	✓ Clean	`N[C@@H](CCC(=O)N[C@@H](CO)C(=O)O)C(=O)O`
ZINC1576203	0.563	261.2 Da LogP -2.50 TPSA 158.8	✓ Ro5	✓ Clean	`N[C@@H](CCC(=O)NCC(=O)NCC(=O)O)C(=O)O`
ZINC2516116	0.563	275.3 Da LogP -1.12 TPSA 155.7	✓ Ro5	✓ Clean	`N[C@@H](CCCCNC(=O)CC[C@H](N)C(=O)O)C(=O)O`
ZINC4545887	0.563	275.3 Da LogP -1.12 TPSA 155.7	✓ Ro5	✓ Clean	`N[C@@H](CCCCNC(=O)CC[C@@H](N)C(=O)O)C(=O)O`
ZINC4545888	0.563	275.3 Da LogP -1.12 TPSA 155.7	✓ Ro5	✓ Clean	`N[C@@H](CCC(=O)NCCCC[C@@H](N)C(=O)O)C(=O)O`
ZINC4545889	0.563	275.3 Da LogP -1.12 TPSA 155.7	✓ Ro5	✓ Clean	`N[C@H](CCCCNC(=O)CC[C@@H](N)C(=O)O)C(=O)O`
ZINC1581634	0.552	203.2 Da LogP -2.22 TPSA 135.5	✓ Ro5	✓ Clean	`NC(=O)CC[C@H](N)C(=O)NCC(=O)O`
ZINC5500823	0.552	203.2 Da LogP -2.22 TPSA 135.5	✓ Ro5	✓ Clean	`NC(=O)CC[C@@H](N)C(=O)NCC(=O)O`
ZINC2242694	0.545	276.2 Da LogP -1.39 TPSA 167.0	✓ Ro5	✓ Clean	`N[C@@H](CCC(=O)N[C@@H](CCC(=O)O)C(=O)O)C(=O)O`
ZINC2547582	0.545	276.2 Da LogP -1.39 TPSA 167.0	✓ Ro5	✓ Clean	`N[C@@H](CCC(=O)N[C@H](CCC(=O)O)C(=O)O)C(=O)O`
ZINC3870040	0.545	250.3 Da LogP -1.32 TPSA 129.7	✓ Ro5	✓ Clean	`N[C@@H](CCC(=O)N[C@@H](CS)C(=O)O)C(=O)O`
ZINC3870041	0.545	250.3 Da LogP -1.32 TPSA 129.7	✓ Ro5	✓ Clean	`N[C@@H](CCC(=O)N[C@H](CS)C(=O)O)C(=O)O`
ZINC3870042	0.545	250.3 Da LogP -1.32 TPSA 129.7	✓ Ro5	✓ Clean	`N[C@H](CCC(=O)N[C@@H](CS)C(=O)O)C(=O)O`
ZINC3870043	0.545	250.3 Da LogP -1.32 TPSA 129.7	✓ Ro5	✓ Clean	`N[C@H](CCC(=O)N[C@H](CS)C(=O)O)C(=O)O`
ZINC3872193	0.545	240.2 Da LogP -1.86 TPSA 146.8	✓ Ro5	✓ Clean	`N[C@H](CCC(=O)NCS(=O)(=O)O)C(=O)O`
ZINC4096970	0.545	405.4 Da LogP -2.04 TPSA 233.4	1 viol.	✓ Clean	`N[C@@H](CCC(=O)N[C@@H](CCC(=O)N[C@@H](CCC(=O)O)…`
ZINC4545890	0.545	276.2 Da LogP -1.39 TPSA 167.0	✓ Ro5	✓ Clean	`N[C@H](CCC(=O)N[C@@H](CCC(=O)O)C(=O)O)C(=O)O`
ZINC4545891	0.545	276.2 Da LogP -1.39 TPSA 167.0	✓ Ro5	✓ Clean	`N[C@H](CCC(=O)N[C@H](CCC(=O)O)C(=O)O)C(=O)O`
ZINC2560992	0.531	275.3 Da LogP -1.99 TPSA 172.8	✓ Ro5	✓ Clean	`NC(=O)CC[C@H](N)C(=O)N[C@@H](CCC(=O)O)C(=O)O`
ZINC12954078	0.529	222.2 Da LogP 0.82 TPSA 92.4	✓ Ro5	✓ Clean	`N[C@@H](CCC(=O)Nc1ccccc1)C(=O)O`
ZINC12954085	0.529	222.2 Da LogP 0.82 TPSA 92.4	✓ Ro5	✓ Clean	`N[C@H](CCC(=O)Nc1ccccc1)C(=O)O`
ZINC2106542	0.519	245.3 Da LogP 1.99 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCCCCCCC(=O)O)C(=O)O`
ZINC2106543	0.519	245.3 Da LogP 1.99 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@H](CCCCCCCCCC(=O)O)C(=O)O`
ZINC2108713	0.519	217.3 Da LogP 1.21 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@@H](CCCCCCCC(=O)O)C(=O)O`
ZINC2108714	0.519	217.3 Da LogP 1.21 TPSA 100.6	✓ Ro5	✓ Clean	`N[C@H](CCCCCCCC(=O)O)C(=O)O`

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.